The MicroArray Explorer or MAExplorer is an open source Java-based data mining tool for exploring microarray DNA expression data across multiple hybridized microarrays. Arrays are used to monitor expression profiles under various physiological conditions. MAExplorer is available as a stand-alone application on a user's computer. It read data on the user's disk for creating custom data mining sessions which may be checkpointed for later use. It can handle data derived from a variety of microarrays, with 33P, Cy3/Cy5, and other labeling systems. A data conversion wizard program Cvt2Mae converts tab-delimited array data for use by MAExplorer. Data may be viewed and directly manipulated in images, scatter plots, histograms, expression profile plots, cluster analysis, etc. Interesting sets of clones may be discovered using a "data filter" that finds a set of clones passing a variety of user-specified tests. Users may generate filtered clone reports which may directly access UniGene, GeneBank, NCI/CIT mAdb and other Internet databases. Report data may be exported to Excel. MAExplorer helps: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns for multiple arrays. Data is read from local files on a user's computer or downloaded from a Web array database server. The Web site http://maexplorer.sourceforge.net/ with a local mirror site at http://www.lecb.ncifcrf.gov/MAExplorer. Users may to freely download the stand-alone version of MAExplorer for running on Windows, Macintosh or Unix systems (Sun Solaris, Linux, etc.) as well as providing documentation and tutorials. The source code is available for review or modification using the CVS system of SourceForge.net. A Java plugin facility, MAEPlugins, allows investigators to add their own analysis methods.